The yeast ADA proteins and TBP-class of SPT proteins interact in multiple complexes (ADA/SPT complexes) that are required for the activation and repression of transcription. We have identified Tra1 as a component of these regulatory complexes through the tandem mass spectrometry analysis of proeints that associate with Ngg1/Ada3. Tra1 is a member of a group of putative protein kinases, that have acarboxyl-terminal region related to phosphatidylinisitol 3-kinases. The interaction between Tra1 and ADA/SPT components was verified by the reciprocal coimmiunprecipitation of HA-Ada2 and myc-Tra1 from whole cell extracts in one or complexes also containing Spt7. The association of Tra1 with more that one ADA/SPT complex was suggested by its cofractionation with Ada2, Ngg1 and Spt7 in two separate peaks on a FPLC mono Q column. In the absence of Ada2, the elution profile of Tra1p shifted to a single distinct peak. Tra1 also copurified with ADA/SPT proteins on a DNA-cellulose column where the binding of Tra1 to DNA-cellulose required the ADA components. As well as allowing the initial determination of Tra1p within the ADA/SPT complexes the tandem mass spectrometry analysis identified a phosphopeptide located near the protein's amino-terminus.